Performance evaluation system has vital importance for businesses to maintain their activities effectively. Therefore, one has to be careful while changing the performance evaluation system. Because the changes in performance evaluation system has an impact on individual and organizational performances. Between years 2010-2014 the Ministry of Health of Turkey made changes in performance evaluation system three times. In this study, the last changes in evaluation system and its their effects on individual and organizational performances were examined at Kocaeli University Research and Training Hospital, in terms of variables such as medical examination and the number of operations numbers and income levels.